The invention provides a method for producing natural carotenoid by cultivating deinococcus radiodurans, which is obtained through collection of soybean whey, edulocration, adjusting of potential of hydrogen (pH), culture adding, sterilization, activation of strain, seed cultivation, fermenting and cultivation, wall-breaking of thallus, extraction of carotenoid and preparation of dried products. The method utilizes by-product of the soybean whey in a processing process of soya bean products such as bean curd to cultivate bacteria to ferment and produce the natural carotenoid, achieves waste recovery of the soybean whey, improves resource use efficiency, reduces pollution on environment caused by soya bean product processing enterprises, and is favorable for protecting environment. 229.8 mg carotenoid dried products can be obtained from per liter of the soybean whey fermentation broth and are 226.2% higher than carotenoid dried products obtained through a conventional cultivation fermenting extraction method. In the method, processing of acid-heating and wall-breaking is firstly conducted on somatic cells, then ethanol is used for extraction, and the extraction is complete and fast. The method is simple in production technology process, low in production cost. Products are free of toxic residue and high in safety.